--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Mon Nov 21 11:12:59 WET 2016 codeml.models=0 1 2 3 7 8 mrbayes.mpich= mrbayes.ngen=1000000 tcoffee.alignMethod=CLUSTALW2 tcoffee.params= tcoffee.maxSeqs=0 codeml.bin=codeml mrbayes.tburnin=2500 codeml.dir= input.sequences= mrbayes.pburnin=2500 mrbayes.bin=mb_adops tcoffee.bin=t_coffee_ADOPS mrbayes.dir=/usr/bin/ tcoffee.dir= tcoffee.minScore=3 input.fasta=/opt/ADOPS/3/ACC-PA/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/3/ACC-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/ACC-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": (Use the harmonic mean for Bayes factor comparisons of models) (Values are saved to the file /opt/ADOPS/3/ACC-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -27181.50 -27199.41 2 -27180.94 -27200.89 -------------------------------------- TOTAL -27181.18 -27200.41 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/3/ACC-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/ACC-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": Summaries are based on a total of 3002 samples from 2 runs. Each run produced 2001 samples of which 1501 samples were included. Parameter summaries saved to file "/opt/ADOPS/3/ACC-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.367052 0.001374 1.295392 1.437846 1.367623 1145.49 1294.57 1.000 r(A<->C){all} 0.076491 0.000031 0.065520 0.087155 0.076484 1109.57 1178.82 1.000 r(A<->G){all} 0.313719 0.000132 0.292233 0.336622 0.313664 726.38 801.23 1.000 r(A<->T){all} 0.117651 0.000073 0.100219 0.132995 0.117641 697.21 855.65 1.000 r(C<->G){all} 0.039814 0.000010 0.034035 0.046258 0.039728 1089.46 1185.48 1.000 r(C<->T){all} 0.387968 0.000148 0.364154 0.412316 0.387805 704.75 715.87 1.000 r(G<->T){all} 0.064356 0.000025 0.054700 0.074167 0.064440 826.32 984.77 1.000 pi(A){all} 0.221872 0.000020 0.213027 0.230319 0.221802 630.90 820.16 1.000 pi(C){all} 0.286470 0.000023 0.276865 0.295084 0.286480 952.43 1042.94 1.000 pi(G){all} 0.279060 0.000023 0.270004 0.288737 0.279092 858.66 882.99 1.000 pi(T){all} 0.212599 0.000017 0.204295 0.220242 0.212615 693.29 828.86 1.001 alpha{1,2} 0.104131 0.000012 0.097563 0.111219 0.104104 1063.23 1178.46 1.000 alpha{3} 8.697463 1.942946 6.302670 11.574470 8.572163 1501.00 1501.00 1.000 pinvar{all} 0.316242 0.000177 0.290012 0.342428 0.316307 1407.62 1454.31 1.000 ------------------------------------------------------------------------------------------------------ * Convergence diagnostic (ESS = Estimated Sample Size); min and avg values correspond to minimal and average ESS among runs. ESS value below 100 may indicate that the parameter is undersampled. + Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman and Rubin, 1992) should approach 1.0 as runs converge. Setting sumt conformat to Simple --- CODEML SUMMARY Model 1: NearlyNeutral -25004.541935 Model 2: PositiveSelection -25004.54212 Model 0: one-ratio -25175.679924 Model 3: discrete -24947.134825 Model 7: beta -24958.012288 Model 8: beta&w>1 -24948.97525 Model 0 vs 1 342.27597799999785 Model 2 vs 1 3.699999942909926E-4 Model 8 vs 7 18.074076000004425 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: D_melanogaster_ACC-PA) Pr(w>1) post mean +- SE for w 34 S 0.901 1.413 +- 0.271 46 G 0.624 1.155 +- 0.459 70 P 0.988* 1.491 +- 0.088 73 P 0.872 1.386 +- 0.308 899 S 0.617 1.142 +- 0.469 962 L 0.822 1.344 +- 0.347